6CJ9

Crystal structure of lectin from Dioclea lasiophylla seeds (DlyL) complexed with X-Man

• PDB DOI: https://doi.org/10.2210/pdb6CJ9/pdb
• Entry: 6CJ9 supersedes: 5U37

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Dioclea lasiophylla
• Mutation(s): No 


• Deposited: 2018-02-26 Released: 2018-03-07 
• Deposition Author(s): Pinto-Junior, V.R., Santiago, M.Q., Osterne, V.J.S., Araripe, D.A., Neco, A.H.B., Silva-Filho, J.C., Leal, R.B., Rocha, C.R.C., Nascimento, K.S., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Crystal structure of DlyL, a mannose-specific lectin from Dioclea lasiophylla Mart. Ex Benth seeds that display cytotoxic effects against C6 glioma cells.

Leal, R.B., Pinto-Junior, V.R., Osterne, V.J.S., Wolin, I.A.V., Nascimento, A.P.M., Neco, A.H.B., Araripe, D.A., Welter, P.G., Neto, C.C., Correia, J.L.A., Rocha, C.R.C., Nascimento, K.S., Cavada, B.S.

(2018) Int J Biol Macromol 114: 64-76

• PubMed: 29559315 
• DOI: https://doi.org/10.1016/j.ijbiomac.2018.03.080
• Primary Citation of Related Structures:  
  6CJ9

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Organizational Affiliation: 

Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 25.92 kDa 
• Atom Count: 2,072 
• Modelled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A	237	Dioclea lasiophylla	Mutation(s): 0
UniProt
Find proteins for C0HK27 (Dioclea lasiophylla) Explore C0HK27  Go to UniProtKB:  C0HK27

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XMM	D [auth A]	5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside C14 H15 Br Cl N O6 OPIFSICVWOWJMJ-HAAGFXOZSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.1	α = 90
b = 86.93	β = 90
c = 92.82	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Pinto-Junior, V.R., Santiago, M.Q., Osterne, V.J.S., Araripe, D.A., Neco, A.H.B., Silva-Filho, J.C., Leal, R.B., Rocha, C.R.C., Nascimento, K.S., Cavada, B.S.
• This entry supersedes: 5U37

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary